The Mess I Made
by pride97
Summary: Tom and Rachel navigate a changing relationship in the midst of the virus mutating. Post season 2. Tom/Rachel with a dose of Sasha/Rachel friendship.
1. Chapter 1

The Mess I Made chapter 1

Pairing: Tom/Rachel, Rachel/Sasha friendship

Rating: T (possibly M for language).

Disclaimer: I own nothing because if I did, 1) Rachel would have never been killed off and 2) we would already know the premiere date for season 5.

Author's Note: I really loved writing the Sasha/Rachel friendship in my other fiction, Up in Smoke. For the purpose of this fiction my timeline (at bottom) for season 1 and season 2 are what I'm using. Anything after Rachel is shot is going to be changed.

Don't worry I haven't abandoned Come For You. I've got 7 chapters written and am working on the last chapter but this little plot bunny came to my mind and I had to start writing!

* * *

 _Something about you_

 _It's like a addiction_

 _Hit me with your best shot honey_

 _I've got no reason to doubt you_

 _'Cause some things hurt_

 _And you're my only virtue_

 _And I'm virtually yours_

 _And there's certain things that I adore_

 _And there's certain things that I ignore_

 _But I'm certain that I'm yours_

 _Certain that I'm yours_

 _Certain that I'm yours_

-Certain Things by James Arthur

* * *

 **February 24, 2015**

"Find me"

Tom watched as Rachel smiled, turned and headed towards her room. She stopped abruptly about twenty feet from him.

Tom cocked his head, "Rachel?"

She turned and walked back towards him, determination on her face. She stopped when there was only about a foot between their two bodies.

"Rachel"

Her hands went up and pulled his face towards hers. Their lips met in a consuming kiss. Tom pushed Rachel against the door, fumbling for the key card to get it open. Tom nudged her into the room and closed the door with his foot. Breaking contact for only seconds to breath, the pair quickly divested themselves of their clothing and fell onto the bed.

Tom pushed Rachel's hair out of her face as he slowly entered her. Rachel sighed at the intimate connection their bodies were making. Tom took his time making love to Rachel, bringing them both to euphoria.

* * *

Rachel awoke a hours later as the sun was streaming through the partially open windows. She momentarily forgot where she was, until she realized her body was trapped by another. She turned her head and saw Tom still asleep. She closed her eyes as the memory of last night came rushing back to her.

She knew what she was doing when she kissed him. While she didn't regret last night, she wasn't sure how Tom would feel. She disentangled herself from his arms and went about gathering her clothing and getting dressed. She had just finished zipping up the dress when a voice broke the quietness of the room.

"Rachel."

She turned to see Tom sitting up in bed.

"Hi." She pointed to the window, "I've got to go pack."

Tom got out of bed and put on his boxers. He went over to her.

"Find me when you get back."

She smiled, "I will."

Rachel quickly exited the room. Her thoughts were so consumed with Tom that she didn't notice the man sitting on the floor next to her door until she was feet from him.

"You the doc who created the cure?" the man asked, standing up.

Rachel eyed the man warily and began backing slowly away from him.

"I didn't get it yesterday."

"Well, I'm sure you've been inoculated by now with as many people who have it."

"You sure?"

"Yes, I'm absolutely sure. Even talking to me right now will help."

"That's good to know."

Before Rachel could respond, the man pulled a gun from his jacket and fired. The bullet hit her in on the right side of her body. She screamed and fell to the ground. She saw the man take off running.

 _Stay calm! Stay calm! Stay calm!_

Doors began to open in tandem around her. People came spilling out into the hallway.

"Holy shit!" she heard someone yell. "It's doctor Scott."

She felt pressure being placed on the wound.

 _Stay awake! Stay awake! Stay awake!_

"Rachel it's Danny, stay with us."

"Burk, go get the captain, I believe he is in room thirty three. Miller..Wolf..let's get the building locked down. We need to find this bastard. Kara stay with Rachel until the captain gets here."

"Tom" Rachel muttered.

"Shh Rachel, don't talk." Kara whispered to her, keeping pressure on the wound.

Rachel began to close her eyes.

"Rachel! Rachel! You need to stay awake! Rachel!"

* * *

 **February 26, 2015**

Rachel groaned as she slowly opened her eyes.

"Rachel? Rios! Rachel is coming to!" the voice shouted.

The voice came from next to her, it sounded like Tom's. Where the hell was she? She tried to sit up but a blinding pain shot through her body.

"Don't try to sit up."

The room and person came into focus. Tom was sitting next to her. She looked around, she was on the Nathan James, in the sickbay.

Rios came into the room, Tom moved out of the way for him.

"What?" Rachel started.

"You were shot Rachel." Rios told her. "It was a through and through, but the bullet nicked an artery."

"You were incredibly lucky Rachel. Kara stayed with you putting pressure on the wound. The captain was able to get you to the James within fifteen minutes after you had been shot."

"Tom, thank you." She reached out and took his hand.

"You're welcome." Tom replied squeezing her hand in response.

Rios finished checking Rachel's IV and blood pressure. "You're bp is good, a little low but that is to be expected. You're going to need to keep the IV for at least another twenty four to thirty six hours. We may need to do another blood transfusion as well"

Rachel groaned, "no arguments doctor Scott, we almost lost you." Rios ordered.

Rios left the room. Tom went back over to the chair and sat back down.

"Who shot me?" Rachel asked Tom.

"An immune by the name of Curtis. Green, Miller and Wolf caught him. He is now in custody."

"Why? Why did he want me dead?"

Tom sighed, "while most of the immune leaders took the pardon offered to them by Michener, Curtis followed McDowell and McDowell didn't accept the president's pardon. There really is no good reason Rachel, you created the cure, this went against everything the immunes were prophesying. They just wanted you dead."

"He waited for me."

"What?"

"He was sitting outside my room, waiting for me."

"Jesus Christ Rachel."

"What happens now?"

"Milowski left for Nebraska yesterday. He will be taking over. You will stay in Saint Louis."

"I should be doing my job."

"And you will Rachel. As soon as you are healed and with a full security detail."

Rachel groaned, "I don't need a security detail."

"Rachel you were just shot! You are getting a security detail whether you like it or not. Green, Burk and Tex have already volunteered."

"They have more important things to do than baby-sitting me." Rachel argued.

"Not right now. The James will be going into dry-dock for repairs."

"Let me talk to Jeffrey."

"Who do you think ordered the detail."

"Bloody hell."

"Come on, you better lay back down and get some rest or else Rios will have my ass."

* * *

Rios agrees to let Rachel leave sick-bay the next day, but insists that the IV stay in for another day. Housing was still being arranged for the crew and as her quarters were quite small and she had been using the communal shower, Tom offered to let her take his quarters. This way she had more room to move and her own shower. He stated he would stay in his at sea cabin. Rachel knew arguing with him would be pointless, so instead she just thanked him.

She was sitting in the middle of Tom's bed, going over reports from Milowski when a knock broke her out of her work.

"Come in" she called.

The door opened and in walked Jed, Ashley and Sam. Rachel's face lit up when she saw them.

"Hi! What are you guys doing here?"

"We're moving here!" Sam yelled excitedly and ran over to Rachel. He leaped onto the bed and attempted to give her a hug.

"Be careful there Sammy, she just had surgery." Jed warned his grandson.

"I'm sorry Rachel"

"It's okay Sam, you didn't hurt me."

"Are you okay Rachel?" Ashley whispered from next to Jed.

Rachel looked over to Ashley. Her heart broke as she saw the fear on the young girls face. She patted the open spot next to Sam and Ashley came over.

"I'm going to be okay Ashley. You're dad found me and got me to doc Rios. They fixed me right up. I just need to take it easy for a bit of time."

Ashley nodded.

"So what is this about you guys moving to Saint Louis?" Rachel asked the group.

Jed came in, neglecting to close the door behind him, and took a seat at the chair across from Rachel.

"Well, since Tom will be here as the Chief of Naval Operations, it was only appropriate that we pack up the Norfolk house and make the move here."

"Makes sense."

"Will you be staying here Rachel?" Sam asked.

"Yes. I will be staying in Saint Louis Sam."

"Isn't that awesome Ashley!" Sam exclaimed "We don't have to email or vid-chat with Rachel anymore. We can see her anytime we want."

Ashley smiled at her brothers enthusiasm. She ruffled his hair, "Yes Sam it is pretty awesome."

Ashley and Sam made themselves comfortable on either side of Rachel. She draped her arms around the children, being careful with her right one.

* * *

Jed watched with contentment as his grandchildren began telling Rachel everything that had happened since they last spoke. Rachel ate up every word. Jed looked over to the door and noticed Tom standing there watching the scene. Jed quietly got up and went over to the door, walked out and gently closed it behind him.

"Dad, when did you guys get to town? Why didn't you let me know?"

"We got in about an hour and a half ago. The kids insisted on seeing Rachel. They wanted to make sure she was okay."

Tom nodded. "Why was Sam talking about Rachel emailing them and vid-chatting?"

Jed looked over to Tom slightly confused, "She never told you."

"Told me what?"

"Rachel has been emailing and vid-chatting with the kids since you guys left Norfolk."

"She never told me."

"Don't know what to tell you Tom."

"Why wouldn't she tell me?"

Jed shrugged his shoulders, "you need to talk to her son."

Tom opened the door to his quarters. Jed followed him into the room, he stood back though to watch the interactions between the two adults. He saw a smile spread onto Tom's face watching Rachel with the kids. When Rachel realized Tom was in the room, her face lit up and she smiled back, but the smile disappeared just as quickly when she realized the kids were with her.

"Daddy" Sam and Ashley shouted. They jumped off the bed and ran to their father, who engulfed them in hugs.

"Hey kiddos, why don't we go grab some lunch and come back and visit Rachel later." Jed stated.

The kids groaned, but Tom agreed with his father and told them they could come back later. Tom walked them out of the room, giving them each one more hug. He closed the door behind them and went back to Rachel.

She had turned and was now sitting on the edge of the bed.

"I'm sorry."

"I'm not mad at you Rachel."

"You're not?"

"I'm just wondering why you didn't tell me."

Rachel bit her lip, "I'm not sure. Those two weeks Ashley, Sam and Jed spent on the James, I felt I had to constantly check on them...make sure they were okay. I felt like I owed you that much. When the kids asked me to keep in touch, I just agreed. I was going to tell you, but honestly I just kept putting it off. Then when everything happened with Niels...I thought you would order me to stop communicating with your family and I couldn't. Getting their emails and doing vid-chats...it made me feel like I…"

"Had a family." Tom concluded.

Rachel nodded.

"Thank you for being there for my children Rachel."

Rachel smiled, "Ashley and Sam are amazing. I really care about them. I want you to know that."

"And it's obvious that they care about you. Hell, they were more concerned about seeing you than me."

Rachel smirked, "well I was the one who was just shot."

Tom rolled his eyes and laughed. "Take it easy okay."

"I will"

"I'll stop by and check on you later okay?"

Rachel smiled, "I'll be here."

* * *

 **March 10, 2015**

The next couple of weeks passed in a blur for Tom. He, Jed and the kids were given permanent housing. Rachel was also given permanent housing, with a full security detail. She was recovering well from her surgery. She had to do some physical therapy for her right shoulder, but there would be no permanent damage. As she would no longer be going around the United States teaching doctors how to spread the cure, she was tasked with training med students, who had survived the virus, how to administer the cure so they could be sent around the country and world. Michener also had her begin to set up a CDC in Saint Louis to begin mass production of the cure. While the contagious cure was the way to go, everyone knew the shot version needed to be available for distribution.

Rachel continued to spend time with Ashley and Sam. It warmed Tom's heart to how his children responded to Rachel. They had never spoken about what happened the night before Rachel was shot. Tom wasn't sure how to bring it up to Rachel. He didn't regret them sleeping together, but he wasn't sure if she did.

Right now the three of them were sitting on the patio playing a game of Sorry. Tom stood watching from the kitchen.

"You going to talk to her?" Jed asked his son coming into the kitchen.

Tom turned and gave his dad a confused look, "talk to her about what?"

"Oh...I don't know...maybe how you feel about her."

Tom turned back and looked outside.

"I love you son...but you're an idiot."

Tom turned back to look at his dad, "excuse me."

"You're in love with Rachel."

"I'm not in love with Rachel. I care about her, yes, but…"

"But what?"

"I just lost Darien dad, not even three months ago!"

"And I understand that you are still dealing with that loss. Grieving. But it doesn't change the fact that you are in love with Rachel."

Tom effectively ended the conversation by walking out of the kitchen and heading outside.

"Can I join the next game?"

Sam begged Rachel to say for dinner, which she agreed too. After dinner, while the Jed and the kids were cleaning up, Rachel pulled Tom outside.

"There's something I need to talk to you about." Rachel started.

"Okay."

"You know about the rumors about the virus mutating?"

Tom nodded in affirmation.

"You also know that the Nathan James will be going to Vietnam to deliver the cure and investigate the claim."

Tom didn't like where this conversation was going.

"I've already spoken to Mike and Jeffrey. I will be accompanying the Nathan James to Vietnam when they leave on the thirteenth."

Tom took a breath, "What about the CDC?"

"I have an amazing staff, they'll be fine. I'm needed on the James to determine if in fact the virus has mutated and if so, to create a new cure."

Tom opened his mouth, when Rachel cut him off, "This is done deal Tom. There is nothing you can say to make me change my mind. I need to go with the James. You know that Mike and the crew won't let anything happen to me."

Tom snorted, "You mean you'll actually listen to Mike's orders?"

Rachel smirked, "Well you know…"

Tom pulled her into a hug, "just promise me you'll be safe."

"I promise."

* * *

 **Timeline**

June 2014: Nathan James leaves Norfolk for the Arctic

October 1- November 5, 2014: Nathan James leaves the Arctic to head to Gitmo (12 days at 20 knots, less if faster), couple of days at Gitmo. Episode 4 the ship gets damaged, it takes a week to get to the island (said in episode) and another 7-10 days (10 days for purpose of timeline) to fix ship up. Danny tells Tex that they have known about the virus for almost a month now.

November 5, 2014: Episode 5, Tom does a audio recording home. At this point we know the ship has been gone for 5 months. During this time they were avoiding the Russians (probably doing at most 12 knots to maintain radio silence). They went started towards Costa Rica and then diverted to Nicaragua (4 days), got captured (2 days), got the monkeys. As they had no clear destination in mind and needed to remain close to Nicaragua for Rachel as we know that she would need more monkeys.

December 5-18, 2014: Episode 7, the flashback says "6 months later". They head to Jamaica for the distress call, again probably only traveling 12 knots . Tom and Tex are taken by the Russians (2 days). The trials start. A couple of days were probably needed to get volunteers, do interviews, get blood work back and set up for the trials. The trials lasted 3 days. The ship probably anchored somewhere during the trials near Jamaica. It is 1153 NM to Baltimore, it took them about 3 days to get there and about 3 days to get the ship back. Kara learns she is pregnant, she would at most be 8 weeks.

December 18-February 21, 2015: Season 2- we know the Nathan James didn't leave Baltimore right away as Rachel needed to mass produce the cure and they needed to re-establish order. The James then went to Norfolk and was there a few days to allow crew to leave and look for family members. The ship then traveled to Florida, to the Gulf of Mexico and took out the submarine. Ravit states in episode 10 that Kara is about 16 weeks pregnant, so we know between season 1 episode 10 and season 2 episode 10 about 8 weeks have passed. Episode 13 states that they will be in Vicksburg on the 18th (no month given), Memphis on the 20th and Saint Louis on the 21st.

February 24, 2015: Inauguration Ball, Rachel shot (a season 3 episode states she was shot 12/24, but logically it doesn't make sense, especially with Kara's pregnancy).


	2. Chapter 2

The Mess I Made chapter 2

Pairing: Tom and Rachel with Rachel/Sasha friendship

Rating: T (M possibly for language only)

Disclaimer: Yeah I own nothing. I own original characters.

Author's Notes: Thank you to everyone who has favorited this story and reviewed. I really appreciate it. I'm also making the assumption that while Tom may be the CNO, he can't just "commandeer" a plane to go to Hong Kong and therefore would need to fly commercial. I'm not military so I obviously don't know the protocol for those "higher up" personal and how they get from point A to point B. Just go with it.

I don't own season 3 on DVD and just realized I could watch it on Hulu. I'm going to be pulling events from season 3 into this story, but obviously everything is different as Rachel is alive in my story.

Also, I do have a method to my "madness" when it comes to Rachel and her tirade against Tom at the end of the chapter.

* * *

 _Should've kissed you there_

 _I should've held your face_

 _I should've watched those eyes_

 _Instead of run in place_

 _I should've called you out_

 _I should've said your name_

 _I should've turned around_

 _I should've looked again_

 _But ohh, I'm staring at the mess I made_

 _I'm staring at the mess I made_

 _I'm staring at the mess I made_

 _As you turn, you take your heart and walk away_

-The Mess I Made by Parachute

* * *

 **April 2, 2015, Nathan James, Vietnam**

Rachel stood on the bridge watching as the Nathan James made port in Vietnam. It had taken twenty days for them to travel the over fourteen thousand nautical miles. During the time they were at sea, more and more reports were surfacing that the virus had mutated. Rachel was devastated as people were once again dying. Mike tried to reassure her that once they were in Vietnam, they would get blood samples so she could analyze the mutation and come up with a new cure. What she really wanted to know is how it mutated?

During the twenty days at sea, she emailed Ashley and Sam daily and did vid-chats with them at least three times a week. She hated leaving the kids. They went through a gamut of emotions when she told them she was leaving. They cried, begged her not to leave and both became angry with her. Tom assured her that they did the same thing whenever he left. In the end they both came around, each giving her a gift. Ashley made her a necklace, which she immediately put on. Sam drew her a picture, which she taped up next to her bed. She asked Tom to get a picture of her and the kids together so she could put it as her background on her laptop. While she may not get to talk to the kids daily, she got to see them daily.

"Rachel" Mike said breaking her out of her thoughts, "a word."

She nodded and followed him outside.

"As soon as we have anchored, we'll begin getting ready to head to land."

"Okay."

"Burk, Miller and Green have been assigned as your security detail."

"I expected as much."

"You are to get the samples you need and get back on the ship. Understand."

"What if I need…"

"This isn't a debate Rachel. I promised Tom that I would make sure you are safe. You will get the samples you need with you security detail and get back on the ship."

* * *

 **April 2, 2015, Saint Louis**

"Tom, I'd like you to head to Hong Kong. We need to find out about the virus mutating and how Peng is involved." Michener stated.

"Do we think he is involved?"

"I'm not sure but there have been alarms raised concerning how China has been handling the virus and possible mutation."

"I understand sir. I'd like to take Taylor with me."

Michener agreed and they discussed further details. Tom left fifteen minutes later. He called Taylor, who agreed to accompany him. He then headed back to his office, where he was greeted by Kara, who had taken over as his aide due to her pregnancy.

"Lieutenant Foster, get a flight booked for Taylor and I to Hong Kong."

Kara nodded and went to work. She got him and Taylor a red-eye with a connection in LAX. They would get to Hong Kong early on the morning of the fourth.

Tom didn't stay much longer in the office as he needed to head home to pack. He wasn't looking forward to telling Ashley and Sam. They didn't take the news of Rachel's departure well and now he was leaving for an indeterminate amount of time.

* * *

 **April 4, 2015 Hong Kong**

"Tom, this is President Peng. President Peng, Tom Chandler, Chief of Naval Operations." Sasha Cooper stated making introductions.

Tom shook President Peng's hand.

"President Peng"

"Captain Chandler."

Peng gestured towards a table, the trio headed over and sat down.

"Captain, how can I be of assistance?"

"I wanted to meet with you in person to discuss the reason for the cure not being distributed to your people."

Peng smirked, "What makes you think the cure isn't being distributed."

"We have on good authority that a majority of the cure is sitting in a Chinese warehouse instead of being shipped to other Asian countries who are begging for it."

"This is incorrect."

"Well, that is why I'm here, to ensure that the cure is given to those who need it."

Peng glares at Tom before speaking, "You have no idea what China has been dealing with. We are being attacked by warlords, pirates and other countries."

"I honestly do not care Mr. President. It is no excuse for the cure not going out. People are dying!"

"Maybe if the United States would stop delivering the cure to China's enemies, we wouldn't have this problem." Peng stated and stood up. He nodded towards his security and walked away.

Tom looked over at Sasha, "I'll talk to him." she said and walked away.

Tom got up and headed towards the bar. Before he made it there a woman ran up to him and grabbed his arm.

"Ma'am"

"Vietnam is not responsible!" she exclaimed and quickly ran off into the crowd.

Tom watched her runoff, confused by her remarks. Wolf rushed over to him.

"Sir, I've just received a report that americans have been taken hostage in Vietnam." Wolf stated then lowered his voice, "the report is that it is crew of the Nathan James."

"Do we know who?" Tom asked

"No."

"We need to get to the James as quickly as possible. I'll talk to Sasha, you try to find out more information."

Wolf nodded and walked off.

Tom searched the ballroom for Sasha. His mind running a mile a minute. Mike promised that Rachel wouldn't go anywhere off the ship without a security detail. Was Rachel one of the "Americans" taken hostage? If the kidnappers didn't recognize her right away, they wouldn't know she was British until she spoke. Tom was worried that not only could he lose Mike and crew he thought of as family, but he could lose Rachel.

Tom found Sasha, who told him she had a friend who could get them to the James. Her friend Jessie owned a helicopter. Sasha, Tom and Wolf made it to Jessie's apartment, but they were met by Peng's men at the airport. Sasha and Jessie had to admit that they had been stealing the cure and taking it across the border. While Tom understood why they did what they did, fighting off Peng's men made matters worse. Sasha ended up taking a bullet in her thigh. Wolf applied pressure to the wound while Tom used his belt to clamp off the blood flow.

Jessie was able to make contact with the James letting them know to be prepared for them and to have a doctor ready for Sasha.

* * *

 **April 5, 2015 Nathan James**

The last twenty four hours had been absolute hell for Rachel. Mike, Miller, Mason, Master Chief, Burk, Diaz, Green, Garnett and Rios has been at a party inland. All hell had broken loose and all but Burk and Green had been kidnapped. Granderson had immediately ordered the James' anchor to be pulled up, the crew to battle stations and moved the ship to international waters.

They had just received word from CIC that a helo was inbound. When they were able to raise the helo, the response was full of static. They were able to understand that the pilot was someone by the name of Jessie and she was bringing naval personnel and there were injuries. Rachel grabbed her supplies to triage the injured and made her way to the helipad.

Rachel stood with some enlisted, assigned to doc Rios in sick-bay, as they watched the helicopter approach.

"Let's get the wounded off the helo as quickly and safely as possible. I'll triage over there" Rachel ordered pointing to an area to their left. "Once the patient or patients are stable we'll get them down to medical. Understand?"

The two men, Williams and Anderson, and one woman, Rourke, nodded.

The helo landed. Rachel and the crew ran over as the door opened. Rachel sighed in relief when she saw Tom and noticed that he had no apparent injuries.

"Tom. Are you okay?" Rachel shouted.

"I'm fine. Sasha got hit, bullet to the thigh. I've clamped it off."

"Okay, let's get her off." Rachel ordered. The two men helped Tom get her off the helo. Wolf followed, Rachel made sure he was okay as well, before running over to Sasha.

She asked Tom to release the cloth that was applying pressure, she quickly examined the wound.

"Let's get her to medical, I need to operate to get the bullet out." she ordered. Williams, Anderson, Rourke and Tom lifted up the board and carried Sasha down with Rachel following closely behind.

Once in medical, Tom stood back and watched Rachel work. Williams, Anderson and Rourke worked in tandem, quickly responding to Rachel's orders. Rachel worked quickly at removing the bullet, checking to make sure all veins and arteries were still intact and unaffected and closing the wound. She add an IV antibiotic to Sasha's drip. When all was said and done, she gave directions to Rourke and came over to Tom.

"She'll be okay. I was able to get the bullet out. There were no fragments. No major veins or arteries were affected. She'll need to take it easy for at least a week, but if she's as stubborn as you, I'll probably only get a few days rest out of her."

"Say's the pot to the kettle." Tom responded.

"I distinctly remember you saying that to me after you're shrapnel injury, but I'll have you remember that I followed all the doctors orders after my own shooting."

Tom put up his hands, "no reminders necessary, I remember you followed orders to the t. But I also remember having to remind you daily to follow those orders."

"I still followed them" Rachel shot back and went back to check on Sasha.

Tom sighs and decides to head up to the bridge to speak to Granderson about the situation. He tells Rachel that he'll be back in a few hours to check on Sasha. Rachel nods and waves him off.

* * *

A few hours laters Sasha begins to come out of anesthesia. She is groggy and in pain. Rourke happens to be changing her IV as she comes too and calls Rachel over.

"Sasha. I'm doctor Scott. You were shot."

Sasha looks up to Rachel, "I remember"

"I was able to remove the bullet and there was no permanent damage. No veins or arteries were nicked. You'll make a full recovery. Your leg will be sore for a few days. I'll give you some painkillers."

"How long will I be stuck down here?" Sasha asked.

Rachel laughed as she finished checking Sasha's vitals.

"What?"

"I told Tom that you need at least a week to recover but if you were anything like him, you'd only take a few days. He of course needed to remind me that I'm the exact same way."

"So there are three incredibly stubborn people aboard the Nathan James together." Sasha replied wryly.

"Apparently so." Rachel responded "your bp is good. I've got you on IV fluids and antibiotics to avoid infection. Unfortunately there are no crutches around, so you will need to stay down here for at least one more day, after that you can be released to your quarters. You'll need a round of antibiotics, penicillin most likely, to ensure there is no infection."

Sasha nodded, "Doctor Scott...thank you."

Rachel smiled, "You're welcome. Feel free to call me Rachel."

* * *

 **April 7, 2015 Nathan James**

Rachel made her way down the p-way to Sasha's quarters. She wanted to check her wound and make sure that there was no infection.

Rachel approached her door and heard arguing coming from inside. She knocked and waited. She was surprised when Tom answered.

"Tom"

"Rachel." He responded. He turned to Sasha, "we'll talk later." he told her and quickly left the room.

Rachel entered and shut the door behind her.

"Everything okay?" Rachel asked coming over to Sasha who was laying on the bed.

"Yeah. Tom's just pissed at me."

Rachel laughed, "been there...done that."

Sasha looked over to Rachel with confusion on her face.

Rachel pulled the desk chair over to the bed and began checking Sasha's vitals and the wound.

"I cannot even begin to describe all the arguments Tom and I had during my time on the James. Especially after he learned that I had been lying to him for four months."

"I'm not familiar…" Sasha admitted "I mean I know you were here and you developed the cure."

"I understand. For the four months we were in the arctic, I knew about the virus and I had to keep it a secret. It was only once the Russians became involved that I had to tell Tom the truth. He was.."

"Pissed" Sasha supplied

"To say the least...so we had many arguments. The wound looks good, it's healing nicely. How does it feel when you put weight on it?"

"It's not pleasant but not the worst pain I've ever felt. I can manage."

"Would you like me to increase your painkiller?"

"No. Thanks, though."

Rachel nodded. She began gathering up her supplies and stood up, put the chair back and headed towards the door.

"I met Tom at academy."

Rachel turned, "what?"

"I'm sure you were wondering how Tom and I know each other. We met at academy. We dated for almost two years."

Rachel stood quietly and allowed Sasha to continue.

"I could tell he wanted a more serious relationship...that he was ready to propose. I wasn't ready for marriage yet. So I ended things."

"You don't need too…"

"No. I want too. I know you and Tom are close friends and I don't want you to think that I still have feelings for him. I will obviously always care as he was my first love but I'm not in love with him anymore."

Rachel nodded and went back over to the chair.

"Tom is... complicated."

Sasha laughed, "that he is"

* * *

 **April 12, 2015 Nathan James**

Over the following five days, Rachel and Sasha began to spend more time together. Sasha agreed to Rachel's demand that she limit the weight on her leg for the first forty eight hours. After that, Rachel agreed to walk around the ship with Sasha to get her strength back up. Rachel told Sasha all about the eight months she spent on the Nathan James, including the trials and Niels murder, her pardon and her shooting. She slowly began to open up about her mother's death, medical school and Michael. Sasha spoke more about her time in academy, what she did after graduation, meeting her husband Andrew and how he died from the virus.

Tom would pop in every day to speak to Sasha about the latest updates on the missing crew. At first he seemed surprised that Rachel and Sasha were together, but eventually he came to expect it.

This particular day Rachel and Sasha decided to join Granderson and Tom on the bridge for the daily report. Green and Burk, having not been captured and making their way back to the James, were present as well.

"The island where the crew is being held is located here." Gator said pointing to a map.

"The plan is to take a team on the RHIB to the island and get our men back." Tom told the group.

"I can have my team ready within the hour sir." Danny stated.

"Get them ready." Tom ordered, "I'll disembark with Green and Taylor."

"You can't be serious!"

"Are you kidding!"

Tom looked over to Rachel and Sasha, anger evident on his face for their outbursts.

"Rachel, Sasha, outside. Now!"

The women followed Tom outside. He lead the two women away from the bridge, as he had a feeling this could be a vocal argument between the threesome. Rachel immediately crossed her arms in defiance. Sasha leaned against the bulkhead to get some weight off her leg, the wind whipping her hair.

"Is there a reason you two feel the need to question my decisions in front of the crew?"

"When your decision is highly inappropriate, I'm going to question it." Rachel fumed.

"You can't go. You're the most recognizable face in the world, other than Rachel's, even in Asia." Sasha pointed out.

"So because people know who I am...I'm what? Not supposed to do my job."

"Tom, your job is not to lead this mission. Your job is to be a leader for this crew!" Rachel stated angrily.

"It is my job." Tom yelled back.

"No its not!" Rachel screamed. "How many times did you say I was too valuable. I was too valuable to leave the ship without a detail surrounding me! Every. Single. Time. And now that I'm telling you the same thing…"

Rachel cupped her hands over her face. Tom could tell she was about to start crying out of sheer anger and frustration.

"What if something happens to you? What if you get captured or worse killed? What happens to us?" Rachel asked.

"Granderson is fully capable…"

"That is not an answer." Rachel spat back.

"Tom. What Rachel is getting at...we know Granderson is fully capable of commanding the James...but is she capable of being a leader to this crew? They need a leader. Their CO has been captured. You are all they have." Sasha stated calmly.

"A leader doesn't run and hide when it becomes difficult."

"I'm not asking you to hide. I'm asking you to be logical. I'm asking you not to put yourself at risk." Rachel replied.

"It's part of the job Rachel. This is something I have to …."

"No Tom, it isn't something you have to do. Green is fully capable of leading the op." Sasha pointed out.

"What about Sam and Ashley? What happens to them if something happens to you?" Rachel blurted out.

Tom was taken aback, Rachel had never used Sam and Ashley in an argument of his safety. Plus, she was fully aware of Kara's pregnancy as she had been monitoring Kara while they were at sea.

"Rachel" Tom said sternly.

Rachel looked at him with defiance in her eyes, but he also saw pain and fear.

"I'm sorry...I just...Why the hell did I have to fall in love with you?" Rachel mumbled before turning and walking away.

Tom looked over to Sasha.

"Yeah, she's in love with you Tom and that fact that you haven't realized it by now makes me want to beat the crap out of you. I figured it out within seconds."

"I better talk to her." Tom said and began to follow after her.

Sasha blocked his path, "I know you mean well, but you both need to calm down. I'll go talk to her. Hopefully, I can convince her to come talk to you before you leave. Don't fuck it up."

* * *

Tom headed back to the bridge, gave the official command to Danny and the team and then headed to his quarters.

He always vid-chatted with the kids before a mission, just to see them one last time, just in case. He went to his desk and waited for the video to load.

"Tom!" Jed exclaimed when he saw his son.

"Hey dad, Sam and Ashley there?"

"You just missed them, they went over to a friends house."

Tom sighed

"What's wrong?"

"I'm heading out on a mission in about an hour and I wanted to see them."

"Can't break tradition now can you? I'm sorry son."

Jed looked over Tom's face, "What else is going on?"

"It's Rachel."

Jed smirked, "What happened now between you two?"

"She and Sasha just questioned my judgment in front of the crew about the mission."

"Well knowing both women...sounds about right."

"Dad!"

"I'm guessing Rachel is the one who argued the longest and loudest."

"You guessed right. She even brought up Ashley and Sam as a reason for me not going on the mission. She has never done that before."

"Tom...What is really bothering you? Rachel has questioned your decisions before, this isn't something new for you in regards to her."

Tom sighed, "She said why the hell did I have to fall in love with you."

"Ahh, so now we get to the heart of the matter. You're upset because Rachel admitting that she is in love with you means you have to confront your feelings for her."

"Sasha said she wanted to beat the crap out of me for not picking up on it earlier."

"Tom, I told you a month ago that you were an idiot and I'm telling you again, you're an idiot!"

"Dad!"

"Tom, stop running from it. Stop hiding from it. It isn't something to be ashamed of. You love Rachel and now you know she loves you. End of discussion. The question is what are you doing to do about it. Are you going to continue lying to yourself about your feelings? Are you going to ignore Rachel's declaration of love? Or are you going to man up, stop being an idiot and do something about it."


	3. Chapter 3

The Mess I Made chapter 3

Pairing: Tom/Rachel, Rachel/Sasha friendship

Rating: T (possibly M for language)

Disclaimer: yup still don't own anything.

Author's Notes: Thank you to everyone who has favorited or reviewed. I really appreciate it. I will admit up front that this chapter is kind of sappy. Sorry. I did try to add some humor on the last line. And I have to say, the last line of this chapter is like my favorite line ever! Mainly, because I could see the character saying it.

* * *

 _We build it up, we tear it down_

 _We leave our pieces on the ground_

 _We see no end, we don't know how_

 _We are lost and we're falling_

 _Hold onto me_

 _You're all I have, all I have_

 _Hold onto me_

 _You're all I have, all I have_

-Pieces by Rob Thomas

* * *

Sasha found Rachel in her lab. She made sure the door closed securely behind her. Rachel was sitting at her desk, her head down on her laptop.

"Rachel?"

Rachel looked up, tears streaming down her face.

"That man is infuriating!"

Sasha smirked and walked over to Rachel.

"It comes with the territory."

"But still. Too not even consider the ramifications of his actions."

Sasha pulled up a chair and sat down next to Rachel.

"It's not about ignoring the ramifications it's about getting the job done. That is what has been ingrained into Tom, getting the job done."

When Rachel didn't respond Sasha continued, "I know this whole situation is difficult. And while I don't agree with his decision to go on this mission, I understand where he is coming from."

Rachel sighed in defeat. "I know why he is doing this. This crew, they are his family. He showed this time and time again. It's just….it's just incredibly frustrating."

"Okay, then what is really bothering you about him going?"

Rachel exhaled, "The last mission he went on, it was to an oil rig. A group of immunes launched RPG's at it. He ended up with a severe shrapnel injury. We lost four men...he was almost number five. I almost lost him a couple of times of the table."

"You're worried about him. That is understandable after everything you guys have been through."

Sasha paused, she wasn't sure how to bring up the next topic.

"You want to talk about what you said?" Sasha asked.

Rachel looked at her slightly confused, "You said Why the hell did I have to fall in love with you?"

Rachel buried her face in her hands and put her head back on the laptop, "bloody hell."

"It needed to be said."

Rachel lifted her head back up and stared at Sasha, "No, it really didn't."

Sasha laughed, "Rachel, I've only known you for what...five days now...and I could tell within seconds of you talking about Tom that you were in love with him. How the hell he didn't know is beyond me!"

"Because I've become an expert at keeping my feelings hidden."

"Maybe, to those who aren't paying attention."

Rachel inhaled, "How did he react?"

"He wanted to come after you, but I insisted it be me as you both were too angry at each other."

"Thank you. I know I need to talk to him...I just...I can't yet."

Rachel rubbed her face and Sasha watched as her hands went subconsciously to her abdomen.

Sasha leaned back in her chair. Everything was making sense now. Rachel's reaction to Tom leading the mission, bringing up Ashley and Sam. Sasha thought back through the last couple of days. She had noticed Rachel either nauseous or vomiting a few times. When she asked Rachel about it, Rachel joked it off as "getting her sea legs again" or a "stomach bug."

"You're pregnant aren't you?" Sasha asked. Rachel looked over to her, her face paling a bit.

Sasha stood up and went over to Rachel, "that's why you were worried. It had nothing to do with Tom, the captain, leading the mission but everything to do with Tom, the father of your child, leading the mission."

When Rachel didn't respond, Sasha continued, "Rachel, You need to talk to him. You need to tell him about the baby and you most definitely need to talk about your outburst confession of love, because we both know if you don't, you're going to regret it."

* * *

Taking Sasha's advice, Rachel made her way to Tom's quarters. She stood in front of the door for a few moments before knocking. Tom answered within seconds.

"Rachel"

"Can I come in?"

Tom moved aside and gestured towards the couch. Rachel entered the room, she went over to the couch. She stopped in front of it and turned to face him.

"I wanted to apologize again. I never should have brought up Ashley and Sam. That was completely uncalled for."

"Rachel, I do understand where you were coming from, but I have to do my job. These people are family and I have to do everything within my power to rescue them."

"I know and I respect that. It's one of the things I lov...things are so complicated"

Rachel closed her eyes and took a deep breath.

"I'm not going to apologize for falling in love with you. I will apologize for how I told you. It shouldn't have been in a way that made it seem like I regretted it, I don't. I will never regret the night we spent together, ever."

"You know what I regret Rachel?" Tom asked her. Concern flooded her beautiful brown eyes.

"What?" she mumbled.

"I will regret everyday, for the rest of my life, not admitting to myself and to you that I am in love with you. I was so lost after Darien's death but you were there. This shining beacon. But it felt like a betrayal to Darien, falling in love with you so soon after her death, that I didn't want to admit anything. I will never regret falling in love with you Rachel. I will never regret kissing you back. I will never regret making love to you."

Tears fell from Rachel's eyes as she launched herself into Tom's arms. He wrapped his arms around her, holding on to her for dear life.

"I love you." Rachel muttered against his chest.

"I love you too Rachel."

They stood like this for a few moments before Rachel pulled away and began pacing.

"There's something else I need to tell you." She stated.

"Okay."

She stopped pacing, seeming to gather her courage, "I'm pregnant."

Tom doesn't say anything for a few moments, comprehending what she just told him.

"How long have you known?"

She shrugged her shoulders, "I didn't realize I was pregnant until a couple of weeks ago and it just... didn't seem like something to tell you via email or a vid-chat. It seemed more like a face to face conversation."

"I've been back on the James for six days now Rachel, you could have told me the first day I was back." Tom pointed out.

"Honestly, Tom I was scared. This isn't something we planned, and.." tears began to form in Rachel's eyes, "bloody hormones" she mumbled, "I wasn't sure how you would react and you had other things to worry about."

Tom took the few steps and closed the distance between them. He cupped her face with his hands, "I could never be upset about a baby...our baby."

Rachel lifted her head, leaned up and kissed him. Tom eagerly responded, but broke the kiss before it could get too heated.

Rachel leaned into him, placing her head and hands on his chest, Tom encircled her petite frame.

"Please just promise me you'll make it back. I can't do this alone. I can't raise our baby alone. I can't. I need you there with me, by my side."

Tom kissed the top of her head, "I will do everything in my power to get back to you Rachel. I can promise you that much."

* * *

Rachel stayed with Tom until it was time for him to head to the RHIB. She followed behind him to the deck, standing back and watching as he gave orders to the team.

Sasha came and stood next to her, "I'm guessing that everything went okay?"

"As well as can be expected considering he is going on a dangerous mission and I'm terrified that something will happen."

"But you talked right?"

"Yes, we talked. I told him I loved him and he knows about the baby."

"Please tell me that he finally admitted he loves you too, otherwise I may have to kill him." Sasha responded, emphasizing "may have to kill him".

Rachel laughed, "yes"

"Thank god! I didn't want to have to kill him. Hiding a body wouldn't be the easiest thing to do, especially the body of the CNO."

Rachel burst out laughing. She began laughing so hard tears started running down her face.

"I'm serious. I was ready to kill him. I was ready to take one for the team."

Before Sasha knew what was happening Rachel had her arms around the woman and pulled her into a friendly hug.

"Thank you."

Sasha hugged her back, "you're welcome"

The two women pulled apart to see Tom approaching them, which caused Rachel to start laughing again, Sasha joining in.

"Did I miss something?" Tom asked.

"Nope" "Nothing" the two women stated in unison.

Tom took Rachel's hand and lead her a few feet away. She noticed the team watching them, as they were only about ten feet from them.

"You do know that the team is watching us."

Tom glanced over his shoulder and shrugged.

"What about the fraternization rules?"

"Well technically, I'm not the captain of the James, I'm the CNO and you are a civilian."

Rachel nodded, "this is true."

"Plus, you know, you're already pregnant."

"Also true."

"Now I'm not saying we can start making out in public, but I don't think there is any harm in this." Tom stated as he pulled her body to his and embraced her.

"I love you." Rachel said "please be safe and come back to me, Ashley, Sam and our baby."

"I love you too. I will come back. I promise you." Tom said and pulled away from Rachel.

He gave her a kiss on the forehead and walked over to the team, who Rachel saw all had knowing smiles on their face.

"You all owe me fifty bucks" Danny told the team, who groaned in response as they climbed into the RHIB.


	4. Chapter 4

The Mess I Made chapter 4

Pairing: Tom/Rachel, Rachel/Sasha friendship

Rating: T

Disclaimer: yup, still own nothing!

Author's Notes: Thank you to everyone who has reviewed! Just a reminder this fiction is completely AU! I'm taking some aspects from season 3 and using them, but obviously, most of it is completely different. I'm so glad you guys enjoyed chapter 3! Danny and the money was/is my favorite part!

Jennparis: I just thought it would be funny for Danny to say something after observing Tom and Rachel embracing. Danny is highly observant and after being on a ship with a group of people for 6-8 months, you're going to notice things. Even Tex, who stated in episode 12 (I believe) of season 2 that Rachel and Tom would talk says something, as Tex has been very vocal about his feelings for her. If Tex can see that there is something between Tom and Rachel, we know Danny would too.

* * *

 _I hear your sighs_

 _I hear your heartbeat_

 _Pound me on my back,_

 _I'm on my own now._

 _What do I see,_

 _What do I feel,_

 _What do I love,_

 _What do I love,_

 _What do I love?_

-Gone by Jessica Riddle

* * *

The hours pass slowly for Rachel. She tries to keep her mind busy by analyzing the blood samples she collected, but she was unable to remain focused. Sasha remained on the bridge for a short period of time, but she eventually headed down to the lab to check on Rachel.

"Rachel" Sasha said to her as she entered the lab, "have you eaten today?"

Rachel looked up from her computer, "I know I should...but I"

"Morning sickness or because you're too focused on your work?"

When Rachel didn't answer, Sasha went over, closed the laptop (much to Rachel's chagrin), pulled Rachel from the chair and began pushing her out of the lab.

"For a doctor, you should know better. You need to keep your strength up not only for yourself but for the baby. You need to eat. No arguments."

* * *

Sasha dragged Rachel down to the enlisted mess hall, as they both knew that the Wardroom would be deserted as a majority of the officers were either on the mission or captured. As the entered the conversations died down, as it was unusual for officers or Doctor Scott to eat down there.

The enlisted watched as Sasha forced Rachel to get a plate of food. The two women ended up sitting at a table with a group of enlisted, which shocked them even further.

"Ma'am, Doctor Scott." The crew said to them as they sat.

"No rank here guys."

The four men and two women nodded their heads.

"Is there any word from the captain?" one of the men, Rhomerson, asked.

"Prior to leaving the bridge" Sasha paused to look at her watch, "approximately fifteen minutes ago, there hadn't been."

The group looked a little crestfallen at her answer, so she quickly added, "but this isn't uncommon. It would the team time to get the RHIB to the island and from what we are aware, the compound where the crew is being held is about five clicks in. Burk is monitoring the team in CIC."

"Doctor Scott" one of the women spoke, to which Rachel looked up from her food, "I wanted to let you know that I was very happy to learn that you survived your shooting and that you are doing okay."

The group echoed her sentiments.

Rachel smiled, "Thank you. It was...terrifying. Those moments, I honestly thought I was going to die. I'm incredibly thankful to Lieutenant's Green and Foster for their quick thinking. I'm also incredibly grateful to the captain and Doc. Rios."

The enlisted finished up their meal and headed back to their respective duty stations, leaving Sasha and Rachel alone.

"This is new to me." Rachel admitted.

Sasha cocked her head, "pardon me?"

"Tom, he would constantly go on missions. It was unspoken that he would be part of the mission. I would worry about him, but more in the aspect of "this is our leader, he needs to make it back okay". But now…"

Sasha reached over and grabbed Rachel's hand. "Hey, I'm here for you. And this Tom. He will move heaven and earth to make it back to you, Ashley, Sam and Jed." Sasha lowered her voice before continuing to speak "and the baby."

Rachel smiled and squeezed Sasha's hand in return. The women continued chatting and were finishing up their lunch when an ensign ran into the room.

"Commander Cooper, Doctor Scott. The XO needs you guys in CIC immediately."

Rachel and Sasha jumped up from the table and quickly disposed of their trays. The followed the ensign to CIC. They found Burk and Granderson talking as they entered.

Alicia waved the women over to her.

"We've got a problem?" Granderson told them.

"What's wrong?" Sasha asked.

"Cobra team has reported in, but we couldn't seem to raise Vulture team."

"Okay."

"Vulture team is missing."

* * *

Rachel blindly walked down the p-ways. She hadn't waited for Alicia to give more information before walking out of CIC. All she heard was vulture team is missing, which means Tom is missing. Sasha had called after her, but she just held up her hand and walked out.

Rachel stopped when she realized she was standing in front of Tom's cabin. She slowly opened the door and stepped into the room. She closed the door behind her and went to his room. Rachel saw that Tom had placed one of his navy shirts across his chair, not even thinking she stripped off her shirt and put his on, taking in the scent that was so uniquely him. Rachel crawled into the bed and the damn burst, her tears began flowing in earnest. She ended up crying herself to sleep.

Rachel was awoken by a beeping. She groggily sat up and looked around. The clock read 17:32. She had been asleep for a little over four hours. The noise kept coming, she realized it was coming from Tom's desk, his computer to be exact. She went to it and saw it was his video chat. She clicked the icon open and Jed's face appeared on the screen. She immediately remembered that Tom did weekly vid chat's with the kids at this time.

"Rachel...what…"

Rachel shook her head, "Hi Jed."

"Tom's not back yet from the mission is he?"

"No, not yet, so I decided to fill in. I know it's not the same. I apologize, I just was so exhausted, my intention was to take a cat nap, but I ended up falling asleep."

"Wearing his shirt?"

Rachel looked down at what she was wearing and shrugged her shoulders, "It was a little more comfortable to rest in. I figured he wouldn't have minded. How have you been?"

Jed started telling Rachel about his week, when he noticed that she began to look a little green. She kept moving her head to the side and had her hand over her mouth.

"Rachel, you okay?"

"Yeah, I'm fine. Please continue."

"You don't look fine. You coming down with something? Is there a stomach bug going around?"

"No...no...nothing like that. Everybody's healthy."

Jed smirked at her before speaking, "you're pregnant, aren't you?"

Rachel looked at him with surprise on her face, "bloody hell is it tattooed on my forehead!"

Jed laughed, "No, but my wife did have three children and I was around for both of Darien's pregnancies, so I've seen morning sickness, or in some cases all day sickness, first hand."

"I've never been seasick, but being pregnant while on a moving ship has not been much fun."

"Rachel's pregnant?" a voice said from behind Jed.

Jed turned and saw that Ashley and Sam were in the room. Jed got up from the chair and gestured for the kids to come over. Ashley took his seat, while he grabbed another one for Sam. Once the children were settled, he adjusted the camera so Rachel could see all of them.

The kids immediately started bombarding her with questions.

"Who's the father?"

"Will he let you keep talking to us?"

"Does he know about the baby?"

"Will you stop talking to us?"

"Does dad know?"

"Ashley, Sam" Jed finally interrupted, "Give Rachel a chance to answer."

Rachel smiled at Jed.

"First, yes I am pregnant. I'm going to answer Sammy's questions first." Rachel paused before continuing, "I'm always going to be there for you guys. I will always be here to talk whenever you need me understand." Ashley and Sam nodded.

"Who's the father?" Ashley asked her question again.

Rachel closed her eyes for second and took a deep breath. When she opened her eyes she saw a look of understanding on Jed's face. He mouthed "Tom" behind the kids. Rachel nodded in affirmation.

"Ashley, Sam...your dad is the father of my baby and yes, he knows that I'm pregnant."

The children leaned back in their chair, absorbing what Rachel had just told them.

Rachel watched as Ashley's eyes began to fill with tears and anger spread across her face.

"This isn't fair."

"Ashley...your father and I didn't plan this."

"No...my mom just died...no...my dad can't be having a baby with someone else...no." Ashley sobbed. She jumped out of the chair and from the room.

Jed sat down next to Sam, taking his hand. "You doing okay Sammy?"

Sam shrugged his shoulders, "Why isn't dad with you? He should be telling us."

"You're dad is still on his mission." Rachel answered

"Rachel didn't intend to tell us she is pregnant, right now. She probably wanted to wait for your father." Jed told Sam. Rachel nodded at Jed's statement and he continued, "but I figured it out and asked her, which she then confirmed and that is what you overheard."

"I'm gonna go check on Ashley." Sam said. He got up and walked out of the room, closing the door behind him leaving Jed and Rachel alone.

Rachel tried to control her emotions. She knew the kids may take the news badly, but she hadn't expected Ashley to react the way she had.

"Give them some time Rachel."

"I know...I had a feeling they may take the news...badly...but I was hoping for the best."

"They'll come around and once Tom talks to them..." Jed said. "So, how did my son take the news. I've been harping on him to talk to you."

"What do you mean harping on him to talk to me? Talk to me about what?"

"The fact that he's in love with you and that you're in love with him."

"He told you about the fight we had, didn't he?"

"Yup and that you admitted you loved him. I called him an idiot, mind you this is the second time I called him an idiot, and told him that he just needed to accept he is in love with you too."

Rachel giggled, "you called Tom an idiot?"

Jed smiled, "I love my son, but he can be a complete moron."

"We did talk and we both admitted that we love each other."

"About damn time." Jed said "So, you never answered my question, how did Tom take the news of another baby?"

Rachel smiled at the memory, "he told me that he could never be upset about a baby, our baby."

"A baby is never a bad thing, Rachel, especially a Chandler baby." Jed told her.

Rachel burst out laughing.

"It's got parents with brains and good looks, both stubborn as hell though. So right there, I don't envy you and Tom at all."

"Thanks" Rachel replied sarcastically, although she knew he was telling the truth about her and Tom.

"Any word on when Tom'll be back?" Jed asked.

Rachel sighed, "I wish I knew. Hopefully soon."

"I'm sure he will be. He's got you, the kids and the baby to come home to. Tom will fight for that."

Rachel smiled and Jed's comment.

"I'll let you go so I can go check on the kids."

"Bye" Rachel said as Jed ended the chat.

* * *

Rachel pushed back the chair and stood. She went over to the couch and laid down, the conversation she just had replaying through her brain.

She was broken out of her thoughts when the door suddenly opened and Sasha rushed into the room. She quickly sat up.

"I had a feeling you'd be here. Come on, there's something you need to see."

Rachel nodded and followed Sasha out of the room. The women headed through the p-ways, towards CIC.

"What's going on? Has Tom reported in? What about Cobra team?"

"Cobra team is back, they got back about fifteen minutes ago." Sasha replied.

They entered CIC. Burk and Granderson were standing in front of a monitor. Danny and Wolf standing nearby. Sasha nodded and a enlisted sailor pressed some buttons and the missing crew appeared on the screen, including Tom.

Rachel gasped when she saw his face. "Damn it, Tom." she said quietly.

"I am Mike Slattery, captain of the Nathan James, serial number 171811120. I, along with members of my crew are prisoners of war."

"I am Tom Chandler, Chief of Naval Operations, serial number 153511508. I, along with crew members from the Nathan James are prisoners of war."

An Asian man stepped in front of the camera, "Takahaya" Sasha said.

"President Jeffrey Michener. The plague has killed but the United States will kill no more. There are two destroyers docked in Okinawa. These destroyers are to leave with in the next thirty six hours or I will begin killing hostages."

The camera panned back to Tom, "We can confirm that the virus has mutated."

The video shut off.

"We're we able to get a location?" Granderson asked.

"No ma'am" Burk answered.

"Wait a second." Sasha said, "that isn''t Tom's serial number."

"Are you sure?" Granderson asked.

"Yes. I've known Tom since academy, that isn't his number."

Granderson turned to an enlisted and told him to get her the crew manifest. Once she had it in hand, she ordered the video to be played again.

"You're right, they don't match."

The group stood for a moment, pondering what the numbers meant. When Green spoke up, "I think they may be coordinates ma'am."

"Play the video again" she said and grabbed a writing utensil. She wrote down the numbers the men stated. "I think you're right Green. But not traditional coordinates..star coordinates."

"That will get us within a couple of miles of them, which is a much better search area than what we were using before." Sasha said.

"I think they may use me as a bargaining chip." Rachel suddenly stated. The group turned to her, forgetting she was even there as she had been so quiet.

"What do you mean?" Granderson asked.

"At the end of the video, Tom makes a point of telling us the virus has mutated. Tom wouldn't have said that without a reason."

"If Takahaya's men are sick.." Sasha said.

"There is no way the captain would want you to go to the island Rachel." Danny said.

"I'm not suggesting that. No, I think Tom will find a way to speak to Takahaya. He will inform Takahaya that I'm on the ship. That all I would need is a sample of their blood. I would be able to determine the mutation and modify the vaccine. It would take time, probably a couple of days, but it could be done."

"The captain will offer Rachel creating a new vaccine just for them" Granderson began

"In exchange for them being released." Rachel concluded.

"But what if the captain isn't successful?" Burk questioned.

"I suggest we begin planning an operation to rescue the crew based on the coordinates Captain Chandler and Captain Slattery provided and quickly, I'm sure Takahaya will soon realize that they lied." Sasha stated.

"I'll begin working on an extraction with Cobra team." Danny said and turned to Granderson, "I may need to pull some men to assist."

"Granted. I want an extraction plan within the hour." Granderson ordered. Danny nodded and he and Wolf took off.

"Request permission to be a member of the extraction team." Sasha asked Granderson.

"Doctor Scott?" Granderson pointedly looked at Rachel.

"She's completely healed. She'd be an asset to the team."

"Permission granted."

Sasha nodded at Rachel and left the room.

"How long will you give Tom?" Rachel asked Alicia.

Alicia nudged her head towards the corner, away from the crew in CIC.

"I'm not sure Rachel. I'll give him as long as I can. I do believe that he will try a diplomatic solution, but at some point we may need to use military force to get them back."

"I understand."

"Rachel...either way we will get the crew back, hopefully it is through the captain and diplomatically and not through force."

* * *

Author's Notes: So I went back and redid this chapter. Originally I had Sam and Ashley taking the news of Rachel's pregnancy rather well. Most stories have them taking it well. I wanted to depart from that, because they are only children. Ashley is supposed to be at most 12-13 and Sam is 8-9. They've lost their mother, their father is gone and they being raised by their grandfather. As much as they care about Rachel this is a huge deal. They have already had so much trauma and this is just one more thing.


End file.
